Refactoring mit task runner
This commit is contained in:
parent
c612b1c67c
commit
8005060d10
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@ -1,5 +1,5 @@
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input/*
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output/*
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log/*
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openrefine/
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jq
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input
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lib
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log
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output
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.task
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@ -0,0 +1,85 @@
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# https://taskfile.dev
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version: '3'
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output: 'group'
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vars:
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DATE:
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sh: date +%Y%m%d_%H%M%S
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env:
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REFINE_MEMORY: 8g
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REFINE_ENDPOINT: http://localhost:3334
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tasks:
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default:
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desc: Workflow
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deps: [bibliotheca, mkdir]
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cmds:
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- tasks/03-ba-sachsen.sh "output/02-bibliotheca-main"
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sources:
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- output/02-bibliotheca-main/bibliotheca.csv
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generates:
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- output/03-ba-sachsen/ba-sachsen.pic
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env:
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REFINE_WORKDIR: output/03-ba-sachsen
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REFINE_LOGFILE: log/03-ba-sachsen/{{.DATE}}.log
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glauchau:
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desc: Glauchau
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deps: [mkdir]
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cmds:
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- tasks/01-bibliotheca-pre.sh "input/glauchau.imp"
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sources:
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- input/glauchau.imp
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generates:
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- output/01-bibliotheca-pre/glauchau.tsv
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env:
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REFINE_MEMORY: 6G
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REFINE_ENDPOINT: http://localhost:3334
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REFINE_WORKDIR: output/01-bibliotheca-pre
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REFINE_LOGFILE: log/01-bibliotheca-pre/{{.DATE}}_glauchau.log
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plauen:
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desc: Plauen
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deps: [mkdir]
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cmds:
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- mkdir -p output/01-bibliotheca-pre log/01-bibliotheca-pre
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- tasks/01-bibliotheca-pre.sh "input/plauen.imp"
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sources:
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- input/plauen.imp
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generates:
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- output/01-bibliotheca-pre/plauen.tsv
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env:
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REFINE_MEMORY: 4G
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REFINE_ENDPOINT: http://localhost:3335
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REFINE_WORKDIR: output/01-bibliotheca-pre
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REFINE_LOGFILE: log/01-bibliotheca-pre/{{.DATE}}_plauen.log
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bibliotheca:
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desc: Hauptverarbeitung
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deps: [glauchau, plauen, mkdir]
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cmds:
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- tasks/02-bibliotheca-main.sh "output/01-bibliotheca-pre"
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sources:
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- output/01-bibliotheca-pre/*.tsv
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generates:
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- output/02-bibliotheca-main/bibliotheca.csv
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env:
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REFINE_WORKDIR: output/02-bibliotheca-main
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REFINE_LOGFILE: log/02-bibliotheca-main/{{.DATE}}.log
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mkdir:
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desc: Ordner erstellen
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cmds:
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- mkdir -p output/01-bibliotheca-pre log/01-bibliotheca-pre
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- mkdir -p output/02-bibliotheca-main log/02-bibliotheca-main
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- mkdir -p output/03-ba-sachsen log/03-ba-sachsen
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status:
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- test -d output/01-bibliotheca-pre
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- test -d log/01-bibliotheca-pre
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- test -d output/02-bibliotheca-main
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- test -d log/02-bibliotheca-main
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- test -d output/03-ba-sachsen
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- test -d log/03-ba-sachsen
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@ -1,5 +1,5 @@
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#!/bin/bash
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# bash-refine v1.1.1: bash-refine.sh, Felix Lohmeier, 2020-07-22
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# bash-refine v1.3.2: bash-refine.sh, Felix Lohmeier, 2020-08-01
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# https://gist.github.com/felixlohmeier/d76bd27fbc4b8ab6d683822cdf61f81d
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# license: MIT License https://choosealicense.com/licenses/mit/
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@ -7,14 +7,30 @@
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# ================================== CONFIG ================================== #
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endpoint="http://localhost:3333"
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memory="1400M" # increase to available RAM
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endpoint="${REFINE_ENDPOINT:-http://localhost:3333}"
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memory="${REFINE_MEMORY:-1400M}"
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csrf="${REFINE_CSRF:-true}"
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date="$(date +%Y%m%d_%H%M%S)"
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workspace="output/${date}"
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logfile="${workspace}/${date}.log"
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csrf=true # set to false for OpenRefine < 3.3
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jq="jq" # path to executable
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openrefine="openrefine/refine" # path to executable
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if [[ -n "$(readlink -e "${REFINE_WORKDIR}")" ]]; then
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workdir="$(readlink -e "${REFINE_WORKDIR}")"
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else
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workdir="$(readlink -m "${BASH_SOURCE%/*}/output/${date}")"
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fi
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if [[ -n "$(readlink -f "${REFINE_LOGFILE}")" ]]; then
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logfile="$(readlink -f "${REFINE_LOGFILE}")"
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else
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logfile="$(readlink -m "${BASH_SOURCE%/*}/log/${date}.log")"
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fi
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if [[ -n "$(readlink -e "${REFINE_JQ}")" ]]; then
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jq="$(readlink -e "${REFINE_JQ}")"
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else
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jq="$(readlink -m "${BASH_SOURCE%/*}/lib/jq")"
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fi
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if [[ -n "$(readlink -e "${REFINE_REFINE}")" ]]; then
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refine="$(readlink -e "${REFINE_REFINE}")"
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else
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refine="$(readlink -m "${BASH_SOURCE%/*}/lib/openrefine/refine")"
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fi
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declare -A checkpoints # associative array for stats
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declare -A pids # associative array for monitoring background jobs
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@ -37,28 +53,29 @@ function requirements {
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# download jq and OpenRefine if necessary
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if [[ -z "$(readlink -e "${jq}")" ]]; then
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echo "Download jq..."
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mkdir -p "$(dirname "${jq}")"
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# jq 1.4 has much faster startup time than 1.5 and 1.6
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curl -L --output "${jq}" \
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"https://github.com/stedolan/jq/releases/download/jq-1.4/jq-linux-x86_64"
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chmod +x "${jq}"; echo
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fi
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if [[ -z "$(readlink -e "${openrefine}")" ]]; then
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if [[ -z "$(readlink -e "${refine}")" ]]; then
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echo "Download OpenRefine..."
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mkdir -p "$(dirname "${openrefine}")"
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mkdir -p "$(dirname "${refine}")"
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curl -L --output openrefine.tar.gz \
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"https://github.com/OpenRefine/OpenRefine/releases/download/3.3/openrefine-linux-3.3.tar.gz"
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echo "Install OpenRefine in subdirectory $(dirname "${openrefine}")..."
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tar -xzf openrefine.tar.gz -C "$(dirname "${openrefine}")" --strip 1 --totals
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echo "Install OpenRefine in subdirectory $(dirname "${refine}")..."
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tar -xzf openrefine.tar.gz -C "$(dirname "${refine}")" --strip 1 --totals
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rm -f openrefine.tar.gz
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# do not try to open OpenRefine in browser
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sed -i '$ a JAVA_OPTIONS=-Drefine.headless=true' \
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"$(dirname "${openrefine}")"/refine.ini
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"$(dirname "${refine}")"/refine.ini
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# set min java heap space to allocated memory
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sed -i 's/-Xms$REFINE_MIN_MEMORY/-Xms$REFINE_MEMORY/' \
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"$(dirname "${openrefine}")"/refine
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"$(dirname "${refine}")"/refine
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# set autosave period from 5 minutes to 25 hours
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sed -i 's/#REFINE_AUTOSAVE_PERIOD=60/REFINE_AUTOSAVE_PERIOD=1500/' \
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"$(dirname "${openrefine}")"/refine.ini
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"$(dirname "${refine}")"/refine.ini
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echo
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fi
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}
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# ============================== OPENREFINE API ============================== #
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function refine_start {
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echo "start OpenRefine server..."
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echo "start OpenRefine server..."
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local dir
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dir="$(readlink -f "${workspace}")"
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${openrefine} -v warn -m "${memory}" -p "${endpoint##*:}" -d "${dir}" &
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dir="$(readlink -e "${workdir}")"
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${refine} -v warn -m "${memory}" -p "${endpoint##*:}" -d "${dir}" &
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pid_server=${!}
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timeout 30s bash -c "until curl -s \"${endpoint}\" \
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| cat | grep -q -o 'OpenRefine' ; do sleep 1; done" \
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# kill OpenRefine immediately; SIGKILL (kill -9) prevents saving projects
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{ kill -9 "${pid_server}" && wait "${pid_server}"; } 2>/dev/null
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# delete temporary OpenRefine projects
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(cd "${workspace}" && rm -rf ./*.project* && rm -f workspace.json)
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(cd "${workdir}" && rm -rf ./*.project* && rm -f workspace.json)
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}
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function refine_check {
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}
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function count_output {
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# word count on all files in workspace
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echo "files (number of lines / size in bytes) in ${workspace}..."
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(cd "${workspace}" && wc -c -l ./*)
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# word count on all files in workdir
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echo "files (number of lines / size in bytes) in ${workdir}..."
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(cd "${workdir}" && wc -c -l ./*)
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}
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function init {
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requirements
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# set trap, create directories and tee to log file
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trap 'error "script interrupted!"' HUP INT QUIT TERM
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mkdir -p "${workspace}"
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mkdir -p "${workdir}" "$(dirname "${logfile}")"
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exec &> >(tee -i -a "${logfile}")
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}
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# Alephino Vorverarbeitung
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# - Exporte der fünf Standorte importieren
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# - in Tabellenformat umwandeln
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# - als eine Datei exportieren
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# Alephino
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for i in leipzig riesa; do
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echo "===== ${i} ====="
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date
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openrefine/openrefine-client -P ${port} --create input/${i}-titel.txt --format=fixed-width --columnWidths=5 --columnWidths=1000000 --storeBlankRows=false --encoding=UTF-8 --projectName=${i}-titel
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openrefine/openrefine-client -P ${port} --create input/${i}-exemplare.txt --format=fixed-width --columnWidths=5 --columnWidths=1000000 --storeBlankRows=false --encoding=UTF-8 --projectName=${i}-exemplare
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openrefine/openrefine-client -P ${port} --apply config/alephino-01-titel.json ${i}-titel
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openrefine/openrefine-client -P ${port} --apply config/alephino-01-exemplare-${i}.json ${i}-exemplare
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openrefine/openrefine-client -P ${port} --export --output${workspace}/${date}/${i}.tsv ${i}-exemplare
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echo ""
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done
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# Alephino
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# - ...
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echo "===== Alephino zusammenführen ====="
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date
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zip -j${workspace}/${date}/alephino.zip${workspace}/${date}/riesa.tsv${workspace}/${date}/leipzig.tsv
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openrefine/openrefine-client -P ${port} --create${workspace}/${date}/alephino.zip --format=tsv --encoding=UTF-8 --includeFileSources=true --projectName=alephino
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openrefine/openrefine-client -P ${port} --export --output${workspace}/${date}/alephino.tsv alephino
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main.sh
44
main.sh
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#!/bin/bash
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# Scripte zur Transformation von Bibliotheca und Alephino nach PICA+
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# ================================ ENVIRONMENT =============================== #
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# download task if necessary
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task="$(readlink -m "${BASH_SOURCE%/*}/lib/task")"
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if [[ -z "$(readlink -e "${task}")" ]]; then
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echo "Download task..."
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mkdir -p "$(dirname "${task}")"
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curl -L --output task.tar.gz \
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"https://github.com/go-task/task/releases/download/v3.0.0-preview4/task_linux_amd64.tar.gz"
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tar -xzf task.tar.gz -C "$(dirname "${task}")" task --totals
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rm -f task.tar.gz
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fi
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# make script executable from another directory
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cd "${BASH_SOURCE%/*}/" || exit 1
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# source the main script
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source bash-refine.sh
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# override default config
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memory="8G"
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endpoint="http://localhost:3334"
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# check requirements, set trap, create workspace and tee to logfile
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init
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# ================================= WORKFLOW ================================= #
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checkpoint "Bibliotheca Vorverarbeitung"; echo
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source config/bibliotheca-01.sh
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checkpoint "Bibliotheca Hauptverarbeitung"; echo
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source config/bibliotheca-02.sh
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checkpoint "PICA+ generieren"; echo
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source config/ba-sachsen.sh
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# ================================= STATS ================================= #
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# calculate run time based on checkpoints
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checkpoint_stats; echo
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# word count on all files in workspace
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count_output
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# execute default task (cf. Taskfile.yml)
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"${task}"
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#!/bin/bash
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# Bibliotheca Vorverarbeitung
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# - Exporte der fünf Standorte importieren
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# - Export von einer der Bibliotheken importieren
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# - in Tabellenformat umwandeln
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# - als eine Datei exportieren
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# - als TSV exportieren
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# ================================== CONFIG ================================== #
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# =============================== ENVIRONMENT ================================ #
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projects["bautzen"]="input/bautzen.imp"
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projects["breitenbrunn"]="input/breitenbrunn.imp"
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projects["dresden"]="input/dresden.imp"
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projects["glauchau"]="input/glauchau.imp"
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projects["plauen"]="input/plauen.imp"
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# source the main script
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source "${BASH_SOURCE%/*}/../bash-refine.sh" || exit 1
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# ================================ BEGIN LOOP ================================ #
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# read input
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if [[ $1 ]]; then
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p="$(basename "$1" .imp)"
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projects[$p]="$(readlink -e "$1")"
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else
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echo 1>&2 "Please provide path to input file"; exit 1
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fi
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for p in "${!projects[@]}"; do
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# make script executable from another directory
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cd "${BASH_SOURCE%/*}/" || exit 1
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checkpoint "${p}"; echo
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# check requirements, set trap, create workdir and tee to logfile
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init
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# ================================= STARTUP ================================== #
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checkpoint "Startup"; echo
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# start OpenRefine server
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refine_start; echo
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# ================================== IMPORT ================================== #
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checkpoint "Import"; echo
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# Line-based text files
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# Character encoding: ISO-8859-1
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# Store blank rows deaktivieren
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"ignoreLines": 1
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}' \
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"${endpoint}/command/core/create-project-from-upload$(refine_csrf)" \
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> "${workspace}/${p}.id"
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> "${workdir}/${p}.id"
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then
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log "imported ${projects[$p]} as ${p}"
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else
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error "import of ${projects[$p]} failed!"
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fi
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refine_store "${p}" "${workspace}/${p}.id" || error "import of ${p} failed!"
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refine_store "${p}" "${workdir}/${p}.id" || error "import of ${p} failed!"
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echo
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# ================================ TRANSFORM ================================= #
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checkpoint "Transform"; echo
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# -------------------- 01 Mehrzeilige Inhalte extrahieren -------------------- #
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# - Column 1 > Text filter > regular expression aktivieren > ^\* > invert
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@ -485,6 +498,8 @@ echo
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# ================================== EXPORT ================================== #
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checkpoint "Export"; echo
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format="tsv"
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echo "export ${p} to ${format} file..."
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if curl -fs \
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@ -492,9 +507,9 @@ if curl -fs \
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--data format="${format}" \
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--data engine='{"facets":[],"mode":"row-based"}' \
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"${endpoint}/command/core/export-rows" \
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> "${workspace}/${p}.${format}"
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> "${workdir}/${p}.${format}"
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then
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log "exported ${p} (${projects[$p]}) to ${workspace}/${p}.${format}"
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log "exported ${p} (${projects[$p]}) to ${workdir}/${p}.${format}"
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else
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error "export of ${p} (${projects[$p]}) failed!"
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fi
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@ -502,8 +517,13 @@ echo
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# ================================== FINISH ================================== #
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checkpoint "Finish"; echo
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# stop OpenRefine server
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refine_stop; echo
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# ================================= END LOOP ================================= #
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# calculate run time based on checkpoints
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checkpoint_stats; echo
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done
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# word count on all files in workdir
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count_output
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@ -1,28 +1,43 @@
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#!/bin/bash
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# Bibliotheca Hauptverarbeitung
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# - Datenbereinigungen
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# - Mapping auf PICA3
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# - PICA3-Spalten als CSV (via Template) exportieren
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# - PICA3 als CSV (via Template) exportieren
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# ================================== CONFIG ================================== #
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# =============================== ENVIRONMENT ================================ #
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# TSV-Exporte aller Einzelprojekte in ein Zip-Archiv packen
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zip -j "${workspace}/bibliotheca.zip" \
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"${workspace}/bautzen.tsv" \
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"${workspace}/breitenbrunn.tsv" \
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"${workspace}/dresden.tsv" \
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"${workspace}/glauchau.tsv" \
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"${workspace}/plauen.tsv"
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# source the main script
|
||||
source "${BASH_SOURCE%/*}/../bash-refine.sh" || exit 1
|
||||
|
||||
projects["bibliotheca"]="${workspace}/bibliotheca.zip"
|
||||
# read input
|
||||
if [[ $1 ]]; then
|
||||
inputdir="$(readlink -e "$1")"
|
||||
else
|
||||
echo 1>&2 "Please provide path to directory with input file(s)"; exit 1
|
||||
fi
|
||||
|
||||
# make script executable from another directory
|
||||
cd "${BASH_SOURCE%/*}/" || exit 1
|
||||
|
||||
# check requirements, set trap, create workdir and tee to logfile
|
||||
init
|
||||
|
||||
# ================================= STARTUP ================================== #
|
||||
|
||||
checkpoint "Startup"; echo
|
||||
|
||||
# start OpenRefine server
|
||||
refine_start; echo
|
||||
|
||||
# ================================== IMPORT ================================== #
|
||||
|
||||
# Neues Projekt erstellen aus Zip-Archiv
|
||||
checkpoint "Import"; echo
|
||||
|
||||
# TSV-Exporte aller Einzelprojekte in ein Zip-Archiv packen
|
||||
zip -j "${workdir}/bibliotheca.zip" "${inputdir}"/*.tsv
|
||||
projects["bibliotheca"]="${workdir}/bibliotheca.zip"
|
||||
|
||||
# Neues Projekt erstellen aus Zip-Archiv
|
||||
p="bibliotheca"
|
||||
echo "import file" "${projects[$p]}" "..."
|
||||
if curl -fs --write-out "%{redirect_url}\n" \
|
||||
|
@ -35,17 +50,19 @@ if curl -fs --write-out "%{redirect_url}\n" \
|
|||
"separator": "\t"
|
||||
}' \
|
||||
"${endpoint}/command/core/create-project-from-upload$(refine_csrf)" \
|
||||
> "${workspace}/${p}.id"
|
||||
> "${workdir}/${p}.id"
|
||||
then
|
||||
log "imported ${projects[$p]} as ${p}"
|
||||
else
|
||||
error "import of ${projects[$p]} failed!"
|
||||
fi
|
||||
refine_store "${p}" "${workspace}/${p}.id" || error "import of ${p} failed!"
|
||||
refine_store "${p}" "${workdir}/${p}.id" || error "import of ${p} failed!"
|
||||
echo
|
||||
|
||||
# ================================ TRANSFORM ================================= #
|
||||
|
||||
checkpoint "Transform"; echo
|
||||
|
||||
# --------------------------- 01 Spalten sortieren --------------------------- #
|
||||
|
||||
# damit Records-Mode erhalten bleibt
|
||||
|
@ -552,6 +569,8 @@ echo
|
|||
|
||||
# ================================== EXPORT ================================== #
|
||||
|
||||
checkpoint "Export"; echo
|
||||
|
||||
# Export der PICA3-Spalten als CSV
|
||||
format="csv"
|
||||
echo "export ${p} to ${format} file using template..."
|
||||
|
@ -626,9 +645,9 @@ if echo "${template}" | head -c -2 | curl -fs \
|
|||
--data engine='{"facets":[],"mode":"row-based"}' \
|
||||
--data-urlencode template@- \
|
||||
"${endpoint}/command/core/export-rows" \
|
||||
> "${workspace}/${p}.${format}"
|
||||
> "${workdir}/${p}.${format}"
|
||||
then
|
||||
log "exported ${p} (${projects[$p]}) to ${workspace}/${p}.${format}"
|
||||
log "exported ${p} (${projects[$p]}) to ${workdir}/${p}.${format}"
|
||||
else
|
||||
error "export of ${p} (${projects[$p]}) failed!"
|
||||
fi
|
||||
|
@ -636,4 +655,13 @@ echo
|
|||
|
||||
# ================================== FINISH ================================== #
|
||||
|
||||
checkpoint "Finish"; echo
|
||||
|
||||
# stop OpenRefine server
|
||||
refine_stop; echo
|
||||
|
||||
# calculate run time based on checkpoints
|
||||
checkpoint_stats; echo
|
||||
|
||||
# word count on all files in workdir
|
||||
count_output
|
|
@ -1,21 +1,45 @@
|
|||
# Generierung PICA+ aus CSV-Exporten
|
||||
#!/bin/bash
|
||||
# Generierung PICA+
|
||||
# - PPNs anreichern und Exemplare clustern
|
||||
# - als PICA+ exportieren
|
||||
|
||||
# ================================== CONFIG ================================== #
|
||||
# =============================== ENVIRONMENT ================================ #
|
||||
|
||||
# TODO: Zusammenführung mit Alephino
|
||||
zip -j "${workspace}/ba-sachsen.zip" \
|
||||
"${workspace}/bibliotheca.csv"
|
||||
# source the main script
|
||||
source "${BASH_SOURCE%/*}/../bash-refine.sh" || exit 1
|
||||
|
||||
projects["ba-sachsen"]="${workspace}/ba-sachsen.zip"
|
||||
# read input
|
||||
if [[ $1 ]]; then
|
||||
inputdir1="$(readlink -e "$1")"
|
||||
else
|
||||
echo 1>&2 "Please provide path to directory with input file(s)"; exit 1
|
||||
fi
|
||||
if [[ $2 ]]; then
|
||||
inputdir2="$(readlink -e "$2")"
|
||||
fi
|
||||
|
||||
# make script executable from another directory
|
||||
cd "${BASH_SOURCE%/*}/" || exit 1
|
||||
|
||||
# check requirements, set trap, create workdir and tee to logfile
|
||||
init
|
||||
|
||||
# ================================= STARTUP ================================== #
|
||||
|
||||
checkpoint "Startup"; echo
|
||||
|
||||
# start OpenRefine server
|
||||
refine_start; echo
|
||||
|
||||
# ================================== IMPORT ================================== #
|
||||
|
||||
# Neues Projekt erstellen aus Zip-Archiv
|
||||
checkpoint "Import"; echo
|
||||
|
||||
# TODO: Zusammenführung mit Alephino
|
||||
zip -j "${workdir}/ba-sachsen.zip" "${inputdir1}"/*.csv
|
||||
projects["ba-sachsen"]="${workdir}/ba-sachsen.zip"
|
||||
|
||||
# Neues Projekt erstellen aus Zip-Archiv
|
||||
p="ba-sachsen"
|
||||
echo "import file" "${projects[$p]}" "..."
|
||||
if curl -fs --write-out "%{redirect_url}\n" \
|
||||
|
@ -28,17 +52,19 @@ if curl -fs --write-out "%{redirect_url}\n" \
|
|||
"separator": ","
|
||||
}' \
|
||||
"${endpoint}/command/core/create-project-from-upload$(refine_csrf)" \
|
||||
> "${workspace}/${p}.id"
|
||||
> "${workdir}/${p}.id"
|
||||
then
|
||||
log "imported ${projects[$p]} as ${p}"
|
||||
else
|
||||
error "import of ${projects[$p]} failed!"
|
||||
fi
|
||||
refine_store "${p}" "${workspace}/${p}.id" || error "import of ${p} failed!"
|
||||
refine_store "${p}" "${workdir}/${p}.id" || error "import of ${p} failed!"
|
||||
echo
|
||||
|
||||
# ================================ TRANSFORM ================================= #
|
||||
|
||||
checkpoint "Transform"; echo
|
||||
|
||||
# ------------------------ 01 PPN anreichern über ISBN ----------------------- #
|
||||
|
||||
# TODO: Anreicherung für 0110
|
||||
|
@ -377,6 +403,8 @@ echo
|
|||
|
||||
# ================================== EXPORT ================================== #
|
||||
|
||||
checkpoint "Export"; echo
|
||||
|
||||
# Export in PICA+
|
||||
format="pic"
|
||||
echo "export ${p} to pica+ file using template..."
|
||||
|
@ -405,9 +433,9 @@ if echo "${template}" | head -c -2 | curl -fs \
|
|||
--data engine='{"facets":[],"mode":"row-based"}' \
|
||||
--data-urlencode template@- \
|
||||
"${endpoint}/command/core/export-rows" \
|
||||
> "${workspace}/${p}.${format}"
|
||||
> "${workdir}/${p}.${format}"
|
||||
then
|
||||
log "exported ${p} (${projects[$p]}) to ${workspace}/${p}.${format}"
|
||||
log "exported ${p} (${projects[$p]}) to ${workdir}/${p}.${format}"
|
||||
else
|
||||
error "export of ${p} (${projects[$p]}) failed!"
|
||||
fi
|
||||
|
@ -415,4 +443,13 @@ echo
|
|||
|
||||
# ================================== FINISH ================================== #
|
||||
|
||||
checkpoint "Finish"; echo
|
||||
|
||||
# stop OpenRefine server
|
||||
refine_stop; echo
|
||||
|
||||
# calculate run time based on checkpoints
|
||||
checkpoint_stats; echo
|
||||
|
||||
# word count on all files in workdir
|
||||
count_output
|
Loading…
Reference in New Issue